Methods for detecting thrombocytosis using biomarkers

Abstract

The present invention relates to a method to determine the gene expression profile of thrombocytotic sensitive genes. The method comprises the following steps; obtaining hematologic samples from subjects in a training set, analyzing the obtained hematologic samples with a microarray, measuring the expression values of each gene on the microarray, performing analysis to identify differentially expressed genes in the training set among three cohorts of thrombocytosis, obtaining hematologic samples from subjects in an independent testing set, and validating the identity of the differentially expressed genes in the independent testing set among the three cohorts of thrombocytosis. The invention also relates to a method to distinguish thrombocytosis cohorts. The method includes the following steps; obtaining a hematologic sample from a subject, determining gene expression of a biomarker subset, analyzing gene expression of the biomarker subset, and classifying the subject into one of three cohorts.

1 . A method to determine the gene expression profile of genes, the method comprising:
 obtaining hematologic samples from subjects in a training set;   analyzing the obtained hematologic samples with a microarray;   measuring the expression values of each gene on the microarray;   performing analysis to identify a biomarker subset of differentially expressed genes in the training set among three cohorts of thrombocytosis;   obtaining hematologic samples from subjects in an independent testing set; and   validating the identity of the differentially expressed genes in the independent testing set among the three cohorts of thrombocytosis.   
     
     
         2 . The method of  claim 1  wherein 4 differentially expressed genes are identified. 
     
     
         3 . The method of  claim 1  wherein 11 differentially expressed genes are identified. 
     
     
         4 . The method of  claim 1  wherein 15 differentially expressed genes are identified. 
     
     
         5 . The method of  claim 1  wherein 4-15 differentially expressed genes are identified. 
     
     
         6 . The method of  claim 5  wherein the biomarker subset comprises at least 4 of the following genes; WASF3, CTNS, HIST1H2AG, ACOT7, LATPM4B, TGFB2, TPM1, H3F3A, APP, NGFRAP1, CLEC1B, HIST1H1A, SRP72, C20orf103 and CRYM. 
     
     
         7 . The method of  claim 5  wherein the biomarker subset comprises the following genes; HIST1H1A, SRP72, C20orf103 and CRYM. 
     
     
         8 . The method of  claim 1 , wherein the step of measuring the expression values is achieved by measuring fluorescence intensities. 
     
     
         9 . The method of  claim 1 , wherein the step of performing analysis to identify differentially expressed genes is achieved with use of a combination of the Kruskal-Wallis, non-parametric one-way analysis of variance, nonparametric Wilcoxon rank-sum test and Non-Parametric Linear Discriminant Analysis with a leave-one-out cross-validation analysis. 
     
     
         10 . The method of  claim 1 , wherein the step of validating the identity of differentially expressed genes is achieved with use of Non-Parametric Linear Discriminant Analysis with a leave-one-out cross-validation analysis. 
     
     
         11 . A method to distinguish thrombocytosis cohorts, the method including the following steps:
 obtaining a hematologic sample from a subject;   determining gene expression of a biomarker subset;   analyzing gene expression of the biomarker subset; and   classifying the subject into a cohort.   
     
     
         12 . The method of  claim 11  wherein the gene expression of the biomarker subset comprises gene expression of a 4 biomarker subset. 
     
     
         13 . The method of  claim 11  wherein the gene expression of the biomarker subset comprises gene expression of a 11 biomarker subset. 
     
     
         14 . The method of  claim 11  wherein the gene expression of the biomarker subset comprises gene expression of a 15 biomarker subset. 
     
     
         15 . The method of  claim 14  wherein the biomarker subset comprises at least 4 of the following genes; WASF3, CTNS, HIST1H2AG, ACOT7, LATPM4B, TGFB2, TPM1, H3F3A, APP, NGFRAP1, CLEC1B, HIST1HIA, SRP72, C20orf103, and CRYM 
     
     
         16 . The method of  claim 15  wherein the biomarker subset comprises the following genes; HIST1HIA, SRP72, C20orf103, and CRYM 
     
     
         17 . The method of  claim 11  wherein the cohort is selected from the group consisting of: normal subjects, subjects with Essential Thrombocythemia (ET) and subjects with Reactive Thrombocytosis (RT). 
     
     
         18 . The method of  claim 11  wherein the step of determining gene expression is achieved through a microarray. 
     
     
         19 . The method of  claim 11  wherein the step of determining gene expression is achieved through a polymerase chain reaction (PCR). 
     
     
         20 . The method of  claim 19  wherein the PCR is a quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR). 
     
     
         21 . The method of  claim 11  wherein the step of determining gene expression is achieved through a microsphere based platform. 
     
     
         22 . The method of  claim 11  wherein the hematologic sample is whole blood. 
     
     
         23 . The method of  claim 11  wherein the hematologic sample is platelets. 
     
     
         24 . The method of  claim 11  wherein the subject is a human. 
     
     
         25 . The method of  claim 11  wherein the step of classifying the subject into a cohort is achieved by classifying a subject into the cohort with the highest posterior possibility.